Starting phenix.real_space_refine on Fri Mar 6 12:01:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414.map" model { file = "/net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pof_20414/03_2026/6pof_20414_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 20256 2.51 5 N 5360 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "B" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "C" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Chain: "D" Number of atoms: 7906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 1021, 7898 Classifications: {'peptide': 1021} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 971} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 8059 Time building chain proxies: 12.82, per 1000 atoms: 0.41 Number of scatterers: 31624 At special positions: 0 Unit cell: (152.955, 176.715, 158.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 5832 8.00 N 5360 7.00 C 20256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 2.4 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7392 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 32 sheets defined 43.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.649A pdb=" N TYR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.204A pdb=" N LEU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.621A pdb=" N LEU A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 77 through 85 removed outlier: 3.768A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.182A pdb=" N ASP A 141 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.703A pdb=" N ILE A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.623A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 194 " --> pdb=" O ASN A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 6.630A pdb=" N VAL A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.524A pdb=" N ILE A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.091A pdb=" N ILE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.645A pdb=" N THR A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.872A pdb=" N ARG A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.506A pdb=" N GLU A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.102A pdb=" N GLY A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 removed outlier: 3.841A pdb=" N GLY A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 removed outlier: 4.607A pdb=" N PHE A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 562 removed outlier: 3.523A pdb=" N MET A 560 " --> pdb=" O MET A 556 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 562 " --> pdb=" O ASP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.557A pdb=" N SER A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 578 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.819A pdb=" N GLU A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.775A pdb=" N LEU A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 4.202A pdb=" N ILE A 646 " --> pdb=" O MET A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 675 removed outlier: 3.545A pdb=" N ASN A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.558A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 733 removed outlier: 3.590A pdb=" N ILE A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 removed outlier: 3.975A pdb=" N LYS A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 779 " --> pdb=" O LYS A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 783 removed outlier: 3.541A pdb=" N GLY A 783 " --> pdb=" O LYS A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 783' Processing helix chain 'A' and resid 792 through 805 removed outlier: 3.501A pdb=" N ILE A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 831 removed outlier: 3.597A pdb=" N LEU A 831 " --> pdb=" O TRP A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 866 removed outlier: 3.674A pdb=" N VAL A 862 " --> pdb=" O PRO A 858 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 removed outlier: 3.652A pdb=" N TRP A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 896 removed outlier: 3.504A pdb=" N VAL A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 916 removed outlier: 4.033A pdb=" N ASN A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 931 removed outlier: 3.632A pdb=" N THR A 930 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 931 " --> pdb=" O LEU A 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 927 through 931' Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.559A pdb=" N ALA A 941 " --> pdb=" O GLY A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 952 Processing helix chain 'A' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN A 961 " --> pdb=" O MET A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 997 removed outlier: 3.640A pdb=" N ASP A 992 " --> pdb=" O GLN A 988 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 997 " --> pdb=" O TYR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 3.846A pdb=" N ASP A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1009 " --> pdb=" O ASP A1005 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1014 " --> pdb=" O VAL A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1033 Processing helix chain 'A' and resid 1033 through 1038 Processing helix chain 'A' and resid 1046 through 1055 removed outlier: 3.882A pdb=" N GLU A1050 " --> pdb=" O GLU A1046 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1051 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A1055 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1079 removed outlier: 3.573A pdb=" N GLY A1059 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A1066 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 19 removed outlier: 3.673A pdb=" N TYR B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 47 removed outlier: 4.208A pdb=" N LEU B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 51 removed outlier: 3.599A pdb=" N LEU B 51 " --> pdb=" O PRO B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.773A pdb=" N LYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.159A pdb=" N ASP B 141 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL B 142 " --> pdb=" O GLY B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 138 through 142' Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.705A pdb=" N ILE B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 194 removed outlier: 3.624A pdb=" N PHE B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 6.623A pdb=" N VAL B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.546A pdb=" N ILE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.087A pdb=" N ILE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.632A pdb=" N THR B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.884A pdb=" N ARG B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 399 removed outlier: 4.124A pdb=" N GLY B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 395 " --> pdb=" O MET B 391 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 419 removed outlier: 3.814A pdb=" N GLY B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 519 removed outlier: 4.595A pdb=" N PHE B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 removed outlier: 3.522A pdb=" N MET B 560 " --> pdb=" O MET B 556 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 562 " --> pdb=" O ASP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.527A pdb=" N SER B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 578' Processing helix chain 'B' and resid 579 through 584 removed outlier: 3.884A pdb=" N GLU B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 617 removed outlier: 3.774A pdb=" N LEU B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 611 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 649 removed outlier: 4.197A pdb=" N ILE B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.755A pdb=" N SER B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 676 " --> pdb=" O ASN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.520A pdb=" N VAL B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 703 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 733 Processing helix chain 'B' and resid 771 through 779 removed outlier: 3.980A pdb=" N LYS B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 779 " --> pdb=" O LYS B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 783 removed outlier: 3.575A pdb=" N GLY B 783 " --> pdb=" O LYS B 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 780 through 783' Processing helix chain 'B' and resid 792 through 805 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.602A pdb=" N LEU B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 866 removed outlier: 3.661A pdb=" N VAL B 862 " --> pdb=" O PRO B 858 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 863 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 864 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 879 removed outlier: 3.653A pdb=" N TRP B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.517A pdb=" N VAL B 896 " --> pdb=" O MET B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 916 removed outlier: 4.080A pdb=" N ASN B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 910 " --> pdb=" O GLY B 906 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 912 " --> pdb=" O HIS B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.732A pdb=" N THR B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 931 removed outlier: 3.556A pdb=" N THR B 930 " --> pdb=" O GLY B 927 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 931 " --> pdb=" O LEU B 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 927 through 931' Processing helix chain 'B' and resid 937 through 945 removed outlier: 3.572A pdb=" N ALA B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 952 Processing helix chain 'B' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN B 961 " --> pdb=" O MET B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 997 removed outlier: 3.639A pdb=" N ASP B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR B 993 " --> pdb=" O ILE B 989 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS B 997 " --> pdb=" O TYR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1018 removed outlier: 3.852A pdb=" N ASP B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B1013 " --> pdb=" O GLU B1009 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B1014 " --> pdb=" O VAL B1010 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B1016 " --> pdb=" O LYS B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1033 Processing helix chain 'B' and resid 1033 through 1038 Processing helix chain 'B' and resid 1046 through 1055 removed outlier: 3.745A pdb=" N GLU B1050 " --> pdb=" O GLU B1046 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B1051 " --> pdb=" O GLU B1047 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B1052 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B1055 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1079 removed outlier: 3.573A pdb=" N GLY B1059 " --> pdb=" O GLY B1055 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B1066 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B1070 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.654A pdb=" N TYR C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.205A pdb=" N LEU C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.588A pdb=" N LEU C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 77 through 85 removed outlier: 3.725A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 161 through 168 removed outlier: 3.704A pdb=" N ILE C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 194 removed outlier: 3.631A pdb=" N PHE C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 6.596A pdb=" N VAL C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 232 " --> pdb=" O ILE C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 removed outlier: 3.503A pdb=" N ALA C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 295 Processing helix chain 'C' and resid 312 through 327 removed outlier: 4.153A pdb=" N ILE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.648A pdb=" N THR C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 364 removed outlier: 3.866A pdb=" N ARG C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.510A pdb=" N GLU C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 399 removed outlier: 4.104A pdb=" N GLY C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 395 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 419 removed outlier: 3.826A pdb=" N GLY C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 419 " --> pdb=" O VAL C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 519 removed outlier: 4.611A pdb=" N PHE C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 562 removed outlier: 3.521A pdb=" N MET C 560 " --> pdb=" O MET C 556 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 578 removed outlier: 3.534A pdb=" N SER C 577 " --> pdb=" O SER C 574 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 574 through 578' Processing helix chain 'C' and resid 579 through 584 removed outlier: 3.862A pdb=" N GLU C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 617 removed outlier: 3.777A pdb=" N LEU C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS C 611 " --> pdb=" O ARG C 607 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN C 615 " --> pdb=" O LYS C 611 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 649 removed outlier: 4.190A pdb=" N ILE C 646 " --> pdb=" O MET C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 675 removed outlier: 3.581A pdb=" N ASN C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 removed outlier: 3.572A pdb=" N ARG C 703 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 733 removed outlier: 3.607A pdb=" N ILE C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 779 removed outlier: 4.051A pdb=" N LYS C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 779 " --> pdb=" O LYS C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 783 removed outlier: 3.525A pdb=" N GLY C 783 " --> pdb=" O LYS C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 780 through 783' Processing helix chain 'C' and resid 792 through 805 Processing helix chain 'C' and resid 825 through 831 removed outlier: 3.612A pdb=" N LEU C 831 " --> pdb=" O TRP C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 3.656A pdb=" N VAL C 862 " --> pdb=" O PRO C 858 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 863 " --> pdb=" O ILE C 859 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 864 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 879 removed outlier: 3.716A pdb=" N TRP C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 897 removed outlier: 3.547A pdb=" N VAL C 896 " --> pdb=" O MET C 892 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 897 " --> pdb=" O CYS C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 916 removed outlier: 4.062A pdb=" N ASN C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR C 910 " --> pdb=" O GLY C 906 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 912 " --> pdb=" O HIS C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 925 removed outlier: 3.648A pdb=" N THR C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 removed outlier: 3.534A pdb=" N LEU C 929 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 930 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 931 " --> pdb=" O LEU C 928 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 926 through 931' Processing helix chain 'C' and resid 937 through 945 Processing helix chain 'C' and resid 947 through 952 Processing helix chain 'C' and resid 955 through 964 removed outlier: 5.128A pdb=" N ASN C 961 " --> pdb=" O MET C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.639A pdb=" N ASP C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 993 " --> pdb=" O ILE C 989 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS C 997 " --> pdb=" O TYR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1018 removed outlier: 3.837A pdb=" N ASP C1005 " --> pdb=" O THR C1001 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C1009 " --> pdb=" O ASP C1005 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C1013 " --> pdb=" O GLU C1009 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR C1014 " --> pdb=" O VAL C1010 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C1016 " --> pdb=" O LYS C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1033 Processing helix chain 'C' and resid 1033 through 1038 Processing helix chain 'C' and resid 1046 through 1055 removed outlier: 3.722A pdb=" N GLU C1050 " --> pdb=" O GLU C1046 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C1055 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1079 removed outlier: 3.567A pdb=" N GLY C1059 " --> pdb=" O GLY C1055 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C1066 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C1070 " --> pdb=" O SER C1066 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C1071 " --> pdb=" O MET C1067 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C1079 " --> pdb=" O ASP C1075 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.664A pdb=" N TYR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 47 removed outlier: 4.207A pdb=" N LEU D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 removed outlier: 3.628A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.770A pdb=" N LYS D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 138 through 142 removed outlier: 4.155A pdb=" N ASP D 141 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL D 142 " --> pdb=" O GLY D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 138 through 142' Processing helix chain 'D' and resid 161 through 168 removed outlier: 3.701A pdb=" N ILE D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 194 removed outlier: 3.638A pdb=" N PHE D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 194 " --> pdb=" O ASN D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 6.607A pdb=" N VAL D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.540A pdb=" N ILE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 295 Processing helix chain 'D' and resid 312 through 327 removed outlier: 4.082A pdb=" N ILE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 354 removed outlier: 3.669A pdb=" N THR D 353 " --> pdb=" O ASN D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 364 removed outlier: 3.883A pdb=" N ARG D 362 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 371 Processing helix chain 'D' and resid 383 through 399 removed outlier: 4.117A pdb=" N GLY D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 395 " --> pdb=" O MET D 391 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS D 396 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 419 removed outlier: 3.816A pdb=" N GLY D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 519 removed outlier: 4.593A pdb=" N PHE D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 516 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 562 removed outlier: 3.522A pdb=" N MET D 560 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LYS D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 removed outlier: 3.566A pdb=" N SER D 577 " --> pdb=" O SER D 574 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 574 through 578' Processing helix chain 'D' and resid 579 through 584 removed outlier: 3.879A pdb=" N GLU D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 617 removed outlier: 3.782A pdb=" N LEU D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS D 611 " --> pdb=" O ARG D 607 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 615 " --> pdb=" O LYS D 611 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 649 removed outlier: 4.232A pdb=" N ILE D 646 " --> pdb=" O MET D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.745A pdb=" N SER D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 676 " --> pdb=" O ASN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 removed outlier: 3.557A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 733 removed outlier: 3.581A pdb=" N ILE D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 779 removed outlier: 3.975A pdb=" N LYS D 775 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 779 " --> pdb=" O LYS D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 783 removed outlier: 3.571A pdb=" N GLY D 783 " --> pdb=" O LYS D 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 780 through 783' Processing helix chain 'D' and resid 792 through 805 Processing helix chain 'D' and resid 825 through 831 removed outlier: 3.692A pdb=" N LEU D 831 " --> pdb=" O TRP D 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 866 removed outlier: 3.672A pdb=" N VAL D 862 " --> pdb=" O PRO D 858 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 879 removed outlier: 3.502A pdb=" N VAL D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP D 877 " --> pdb=" O LEU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 897 removed outlier: 3.511A pdb=" N VAL D 896 " --> pdb=" O MET D 892 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR D 897 " --> pdb=" O CYS D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 916 removed outlier: 4.062A pdb=" N ASN D 909 " --> pdb=" O SER D 905 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 910 " --> pdb=" O GLY D 906 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 912 " --> pdb=" O HIS D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 945 removed outlier: 3.552A pdb=" N ALA D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 952 Processing helix chain 'D' and resid 955 through 964 removed outlier: 5.124A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 997 removed outlier: 3.648A pdb=" N ASP D 992 " --> pdb=" O GLN D 988 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR D 993 " --> pdb=" O ILE D 989 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D 997 " --> pdb=" O TYR D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1018 removed outlier: 3.851A pdb=" N ASP D1005 " --> pdb=" O THR D1001 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D1013 " --> pdb=" O GLU D1009 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D1014 " --> pdb=" O VAL D1010 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1033 Processing helix chain 'D' and resid 1033 through 1038 Processing helix chain 'D' and resid 1046 through 1055 removed outlier: 3.720A pdb=" N GLU D1050 " --> pdb=" O GLU D1046 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR D1051 " --> pdb=" O GLU D1047 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY D1055 " --> pdb=" O TYR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1079 removed outlier: 3.557A pdb=" N GLY D1059 " --> pdb=" O GLY D1055 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER D1066 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D1070 " --> pdb=" O SER D1066 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D1071 " --> pdb=" O MET D1067 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.630A pdb=" N VAL A 221 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR A 198 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 121 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE A 119 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.630A pdb=" N VAL A 221 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP A 222 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 197 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.419A pdb=" N LEU A 55 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 75 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 268 removed outlier: 4.129A pdb=" N VAL A 279 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 307 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.368A pdb=" N TRP A 276 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 374 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS A 403 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 375 " --> pdb=" O HIS A 403 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE A 405 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 377 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 541 removed outlier: 7.111A pdb=" N ALA A 527 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 553 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 529 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA A 499 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET A 529 " --> pdb=" O ALA A 499 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 501 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A 500 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 595 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 571 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 634 through 635 removed outlier: 6.721A pdb=" N VAL A 657 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 685 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR A 659 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA A 658 " --> pdb=" O VAL A 714 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL B 221 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR B 198 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 121 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE B 119 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL B 221 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP B 222 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 197 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.405A pdb=" N LEU B 55 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B 75 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 268 removed outlier: 4.144A pdb=" N VAL B 279 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR B 307 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 275 through 277 removed outlier: 6.410A pdb=" N TRP B 276 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LYS B 336 " --> pdb=" O THR B 374 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE B 376 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 338 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ARG B 378 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 340 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N HIS B 403 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 375 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE B 405 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 377 " --> pdb=" O PHE B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 537 through 541 removed outlier: 7.105A pdb=" N ALA B 527 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N PHE B 553 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET B 529 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ALA B 499 " --> pdb=" O ALA B 527 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET B 529 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 501 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 500 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 595 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 571 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 634 through 635 removed outlier: 6.519A pdb=" N VAL B 657 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY B 684 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR B 659 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA B 686 " --> pdb=" O TYR B 659 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER B 661 " --> pdb=" O ALA B 686 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA B 658 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.626A pdb=" N VAL C 221 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 198 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 121 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 119 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.626A pdb=" N VAL C 221 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP C 222 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE C 197 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.810A pdb=" N LEU C 55 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C 75 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 268 removed outlier: 4.086A pdb=" N VAL C 279 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 307 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 275 through 277 removed outlier: 6.354A pdb=" N TRP C 276 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS C 336 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE C 376 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU C 338 " --> pdb=" O PHE C 376 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ARG C 378 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 340 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N HIS C 403 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE C 375 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE C 405 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 377 " --> pdb=" O PHE C 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 537 through 541 removed outlier: 7.096A pdb=" N ALA C 527 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE C 553 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET C 529 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA C 499 " --> pdb=" O ALA C 527 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET C 529 " --> pdb=" O ALA C 499 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 501 " --> pdb=" O MET C 529 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 500 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 595 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN C 571 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 634 through 635 removed outlier: 6.516A pdb=" N VAL C 657 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY C 684 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR C 659 " --> pdb=" O GLY C 684 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ALA C 686 " --> pdb=" O TYR C 659 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER C 661 " --> pdb=" O ALA C 686 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA C 658 " --> pdb=" O VAL C 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL D 221 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 121 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE D 119 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.631A pdb=" N VAL D 221 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.406A pdb=" N LEU D 55 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN D 75 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AD2, first strand: chain 'D' and resid 264 through 268 removed outlier: 4.161A pdb=" N VAL D 279 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR D 307 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.406A pdb=" N TRP D 276 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS D 336 " --> pdb=" O THR D 374 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N PHE D 376 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 338 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ARG D 378 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 340 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N HIS D 403 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE D 375 " --> pdb=" O HIS D 403 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE D 405 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 377 " --> pdb=" O PHE D 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 537 through 541 removed outlier: 7.099A pdb=" N ALA D 527 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE D 553 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 529 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA D 499 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N MET D 529 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL D 501 " --> pdb=" O MET D 529 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 500 " --> pdb=" O ILE D 570 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 595 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 571 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 634 through 635 removed outlier: 6.515A pdb=" N VAL D 657 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY D 684 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR D 659 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA D 686 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER D 661 " --> pdb=" O ALA D 686 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA D 658 " --> pdb=" O VAL D 714 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9993 1.34 - 1.46: 6715 1.46 - 1.58: 15320 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 32316 Sorted by residual: bond pdb=" C LYS C 86 " pdb=" N PRO C 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.08e+01 bond pdb=" C LYS A 86 " pdb=" N PRO A 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.03e+01 bond pdb=" C LYS D 86 " pdb=" N PRO D 87 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.02e+01 bond pdb=" N THR B 842 " pdb=" CA THR B 842 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.82e+00 bond pdb=" N THR D 842 " pdb=" CA THR D 842 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.66e+00 ... (remaining 32311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 42558 2.47 - 4.94: 1054 4.94 - 7.41: 111 7.41 - 9.88: 25 9.88 - 12.35: 12 Bond angle restraints: 43760 Sorted by residual: angle pdb=" C MET D 823 " pdb=" N ASP D 824 " pdb=" CA ASP D 824 " ideal model delta sigma weight residual 121.54 133.89 -12.35 1.91e+00 2.74e-01 4.18e+01 angle pdb=" C ILE D 834 " pdb=" N ARG D 835 " pdb=" CA ARG D 835 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.86e+01 angle pdb=" C ILE A 834 " pdb=" N ARG A 835 " pdb=" CA ARG A 835 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ILE B 834 " pdb=" N ARG B 835 " pdb=" CA ARG B 835 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ILE C 834 " pdb=" N ARG C 835 " pdb=" CA ARG C 835 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.83e+01 ... (remaining 43755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 17253 17.34 - 34.68: 1696 34.68 - 52.02: 286 52.02 - 69.35: 52 69.35 - 86.69: 33 Dihedral angle restraints: 19320 sinusoidal: 7680 harmonic: 11640 Sorted by residual: dihedral pdb=" CA GLY C 622 " pdb=" C GLY C 622 " pdb=" N PRO C 623 " pdb=" CA PRO C 623 " ideal model delta harmonic sigma weight residual -180.00 -141.34 -38.66 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA GLY A 622 " pdb=" C GLY A 622 " pdb=" N PRO A 623 " pdb=" CA PRO A 623 " ideal model delta harmonic sigma weight residual 180.00 -141.37 -38.63 0 5.00e+00 4.00e-02 5.97e+01 dihedral pdb=" CA GLY D 622 " pdb=" C GLY D 622 " pdb=" N PRO D 623 " pdb=" CA PRO D 623 " ideal model delta harmonic sigma weight residual 180.00 -141.40 -38.60 0 5.00e+00 4.00e-02 5.96e+01 ... (remaining 19317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4222 0.082 - 0.164: 627 0.164 - 0.246: 32 0.246 - 0.328: 7 0.328 - 0.411: 4 Chirality restraints: 4892 Sorted by residual: chirality pdb=" CB ILE C 834 " pdb=" CA ILE C 834 " pdb=" CG1 ILE C 834 " pdb=" CG2 ILE C 834 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CB ILE B 834 " pdb=" CA ILE B 834 " pdb=" CG1 ILE B 834 " pdb=" CG2 ILE B 834 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB ILE A 834 " pdb=" CA ILE A 834 " pdb=" CG1 ILE A 834 " pdb=" CG2 ILE A 834 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 ... (remaining 4889 not shown) Planarity restraints: 5612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 35 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO C 36 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 35 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO B 36 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 35 " 0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO D 36 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " 0.040 5.00e-02 4.00e+02 ... (remaining 5609 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3042 2.74 - 3.28: 29955 3.28 - 3.82: 52264 3.82 - 4.36: 60978 4.36 - 4.90: 99911 Nonbonded interactions: 246150 Sorted by model distance: nonbonded pdb=" OG1 THR B 925 " pdb=" OG1 THR D 925 " model vdw 2.196 3.040 nonbonded pdb=" O GLY C 622 " pdb=" OG1 THR C 625 " model vdw 2.247 3.040 nonbonded pdb=" O VAL A 921 " pdb=" OG1 THR A 925 " model vdw 2.249 3.040 nonbonded pdb=" O GLY D 622 " pdb=" OG1 THR D 625 " model vdw 2.252 3.040 nonbonded pdb=" O GLY B 622 " pdb=" OG1 THR B 625 " model vdw 2.253 3.040 ... (remaining 246145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'B' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'C' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) selection = (chain 'D' and (resid 2 through 19 or resid 21 through 225 or resid 227 through \ 1099)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 36.280 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 32316 Z= 0.275 Angle : 0.951 12.353 43760 Z= 0.530 Chirality : 0.057 0.411 4892 Planarity : 0.007 0.072 5612 Dihedral : 14.301 86.693 11928 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.58 % Favored : 93.33 % Rotamer: Outliers : 0.39 % Allowed : 5.70 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.10), residues: 4068 helix: -4.19 (0.07), residues: 1544 sheet: -1.54 (0.21), residues: 472 loop : -2.97 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1045 TYR 0.019 0.002 TYR A 319 PHE 0.020 0.002 PHE A 110 TRP 0.014 0.002 TRP A 743 HIS 0.010 0.002 HIS B1072 Details of bonding type rmsd covalent geometry : bond 0.00573 (32316) covalent geometry : angle 0.95052 (43760) hydrogen bonds : bond 0.31456 ( 1004) hydrogen bonds : angle 10.42018 ( 2949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 SER cc_start: 0.6466 (m) cc_final: 0.5919 (t) REVERT: A 306 GLU cc_start: 0.4950 (pt0) cc_final: 0.4726 (pp20) REVERT: A 423 PRO cc_start: 0.7471 (Cg_exo) cc_final: 0.7265 (Cg_endo) REVERT: A 512 MET cc_start: 0.7085 (mtp) cc_final: 0.6733 (ttm) REVERT: A 514 ASP cc_start: 0.8308 (p0) cc_final: 0.8008 (p0) REVERT: A 591 ILE cc_start: 0.6847 (mp) cc_final: 0.6533 (mp) REVERT: A 666 MET cc_start: 0.7853 (ptp) cc_final: 0.7360 (mmp) REVERT: A 857 MET cc_start: 0.7950 (ttm) cc_final: 0.7024 (mtt) REVERT: A 977 VAL cc_start: 0.8549 (t) cc_final: 0.8303 (t) REVERT: B 285 SER cc_start: 0.6552 (m) cc_final: 0.5931 (t) REVERT: B 306 GLU cc_start: 0.4972 (pt0) cc_final: 0.4751 (pp20) REVERT: B 423 PRO cc_start: 0.7489 (Cg_exo) cc_final: 0.7284 (Cg_endo) REVERT: B 512 MET cc_start: 0.7082 (mtp) cc_final: 0.6736 (ttm) REVERT: B 514 ASP cc_start: 0.8312 (p0) cc_final: 0.8005 (p0) REVERT: B 591 ILE cc_start: 0.6847 (mp) cc_final: 0.6473 (mp) REVERT: B 666 MET cc_start: 0.7818 (ptp) cc_final: 0.7232 (mmp) REVERT: B 857 MET cc_start: 0.8048 (ttm) cc_final: 0.7062 (mtt) REVERT: B 881 ARG cc_start: 0.7433 (tpt90) cc_final: 0.6910 (tpt-90) REVERT: B 977 VAL cc_start: 0.8513 (t) cc_final: 0.8221 (t) REVERT: C 167 LYS cc_start: 0.6181 (tttm) cc_final: 0.5858 (tptm) REVERT: C 200 LEU cc_start: 0.7800 (mm) cc_final: 0.7585 (mm) REVERT: C 512 MET cc_start: 0.7126 (mtp) cc_final: 0.6759 (ttm) REVERT: C 514 ASP cc_start: 0.8312 (p0) cc_final: 0.8025 (p0) REVERT: C 591 ILE cc_start: 0.6870 (mp) cc_final: 0.6495 (mp) REVERT: C 698 MET cc_start: 0.7766 (tpt) cc_final: 0.7426 (tpt) REVERT: C 857 MET cc_start: 0.8039 (ttm) cc_final: 0.7049 (mtt) REVERT: C 881 ARG cc_start: 0.7427 (tpt90) cc_final: 0.6874 (tpt-90) REVERT: C 919 ASP cc_start: 0.8573 (p0) cc_final: 0.8329 (p0) REVERT: C 920 LEU cc_start: 0.9168 (tp) cc_final: 0.8885 (tp) REVERT: C 977 VAL cc_start: 0.8515 (t) cc_final: 0.8219 (t) REVERT: C 1063 LEU cc_start: 0.9412 (tp) cc_final: 0.9160 (tt) REVERT: D 285 SER cc_start: 0.6513 (m) cc_final: 0.5872 (t) REVERT: D 423 PRO cc_start: 0.7489 (Cg_exo) cc_final: 0.7280 (Cg_endo) REVERT: D 512 MET cc_start: 0.7100 (mtp) cc_final: 0.6791 (ttm) REVERT: D 514 ASP cc_start: 0.8353 (p0) cc_final: 0.8055 (p0) REVERT: D 591 ILE cc_start: 0.6815 (mp) cc_final: 0.6513 (mp) REVERT: D 666 MET cc_start: 0.7793 (ptp) cc_final: 0.7213 (mmp) REVERT: D 857 MET cc_start: 0.7891 (ttm) cc_final: 0.6937 (mtt) REVERT: D 977 VAL cc_start: 0.8503 (t) cc_final: 0.8261 (t) REVERT: D 1063 LEU cc_start: 0.9452 (tp) cc_final: 0.9182 (tp) outliers start: 5 outliers final: 1 residues processed: 529 average time/residue: 0.2125 time to fit residues: 174.3892 Evaluate side-chains 334 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 GLN A 150 GLN A 190 ASN ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 672 ASN A 961 ASN A1076 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 150 GLN B 190 ASN B 315 GLN ** B 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 961 ASN B1076 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 54 ASN C 75 ASN C 168 HIS C 190 ASN C 671 ASN C 672 ASN C 850 GLN C 961 ASN C1072 HIS C1076 GLN ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 150 GLN D 190 ASN ** D 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 671 ASN D 850 GLN D 961 ASN D1072 HIS D1076 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.156748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.140286 restraints weight = 160520.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.139843 restraints weight = 145731.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.137239 restraints weight = 118904.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.136730 restraints weight = 124395.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.135789 restraints weight = 106227.937| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32316 Z= 0.220 Angle : 0.743 12.345 43760 Z= 0.393 Chirality : 0.049 0.286 4892 Planarity : 0.006 0.069 5612 Dihedral : 6.354 31.560 4428 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.36 % Favored : 92.49 % Rotamer: Outliers : 0.30 % Allowed : 4.39 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.11), residues: 4068 helix: -2.89 (0.10), residues: 1664 sheet: -1.21 (0.21), residues: 532 loop : -2.82 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 729 TYR 0.047 0.003 TYR A 704 PHE 0.019 0.002 PHE C 998 TRP 0.016 0.002 TRP B 743 HIS 0.007 0.001 HIS D 537 Details of bonding type rmsd covalent geometry : bond 0.00495 (32316) covalent geometry : angle 0.74324 (43760) hydrogen bonds : bond 0.04461 ( 1004) hydrogen bonds : angle 6.31531 ( 2949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 PHE cc_start: 0.5155 (m-80) cc_final: 0.4825 (m-10) REVERT: A 31 TYR cc_start: 0.4550 (p90) cc_final: 0.4258 (p90) REVERT: A 512 MET cc_start: 0.7454 (mtp) cc_final: 0.6973 (ttm) REVERT: A 857 MET cc_start: 0.7983 (ttm) cc_final: 0.7514 (mtp) REVERT: A 977 VAL cc_start: 0.8818 (t) cc_final: 0.8592 (t) REVERT: B 29 PHE cc_start: 0.5044 (m-80) cc_final: 0.4688 (m-10) REVERT: B 31 TYR cc_start: 0.4515 (p90) cc_final: 0.4203 (p90) REVERT: B 512 MET cc_start: 0.7454 (mtp) cc_final: 0.6950 (ttm) REVERT: B 857 MET cc_start: 0.8095 (ttm) cc_final: 0.7667 (mtp) REVERT: B 977 VAL cc_start: 0.8706 (t) cc_final: 0.8428 (t) REVERT: C 327 MET cc_start: 0.6739 (ttm) cc_final: 0.6512 (ptp) REVERT: C 512 MET cc_start: 0.7534 (mtp) cc_final: 0.7003 (ttm) REVERT: C 857 MET cc_start: 0.8057 (ttm) cc_final: 0.7360 (mtt) REVERT: C 977 VAL cc_start: 0.8736 (t) cc_final: 0.8467 (t) REVERT: C 1072 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.8352 (m-70) REVERT: D 29 PHE cc_start: 0.5039 (m-80) cc_final: 0.4708 (m-10) REVERT: D 31 TYR cc_start: 0.4482 (p90) cc_final: 0.4176 (p90) REVERT: D 512 MET cc_start: 0.7554 (mtp) cc_final: 0.7014 (ttm) REVERT: D 857 MET cc_start: 0.7971 (ttm) cc_final: 0.7427 (mtt) REVERT: D 919 ASP cc_start: 0.8985 (p0) cc_final: 0.8671 (p0) REVERT: D 977 VAL cc_start: 0.8844 (t) cc_final: 0.8614 (t) REVERT: D 1072 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8342 (m-70) outliers start: 2 outliers final: 0 residues processed: 457 average time/residue: 0.1838 time to fit residues: 138.0245 Evaluate side-chains 332 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 268 optimal weight: 30.0000 chunk 99 optimal weight: 0.8980 chunk 312 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 908 HIS ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 908 HIS C 9 GLN C 908 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 908 HIS D1020 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.156829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140567 restraints weight = 176560.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.139110 restraints weight = 164734.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136489 restraints weight = 137872.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.136305 restraints weight = 133960.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.135775 restraints weight = 100332.734| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32316 Z= 0.193 Angle : 0.698 11.750 43760 Z= 0.368 Chirality : 0.048 0.195 4892 Planarity : 0.005 0.053 5612 Dihedral : 6.050 30.344 4428 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.81 % Favored : 92.09 % Rotamer: Outliers : 0.24 % Allowed : 2.52 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.39 (0.11), residues: 4068 helix: -2.14 (0.11), residues: 1668 sheet: -1.14 (0.22), residues: 532 loop : -2.64 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 881 TYR 0.019 0.002 TYR C 825 PHE 0.016 0.002 PHE C 998 TRP 0.026 0.002 TRP A 827 HIS 0.006 0.001 HIS D1072 Details of bonding type rmsd covalent geometry : bond 0.00437 (32316) covalent geometry : angle 0.69828 (43760) hydrogen bonds : bond 0.04020 ( 1004) hydrogen bonds : angle 5.77228 ( 2949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.7445 (mtp) cc_final: 0.6979 (ttm) REVERT: A 857 MET cc_start: 0.7447 (ttm) cc_final: 0.7038 (mtp) REVERT: A 977 VAL cc_start: 0.8696 (t) cc_final: 0.8430 (t) REVERT: B 512 MET cc_start: 0.7530 (mtp) cc_final: 0.7027 (ttm) REVERT: B 572 PHE cc_start: 0.7866 (m-80) cc_final: 0.7654 (m-80) REVERT: B 857 MET cc_start: 0.7693 (ttm) cc_final: 0.7251 (mtp) REVERT: B 977 VAL cc_start: 0.8609 (t) cc_final: 0.8385 (t) REVERT: C 512 MET cc_start: 0.7669 (mtp) cc_final: 0.7022 (ttm) REVERT: C 857 MET cc_start: 0.7418 (ttm) cc_final: 0.6734 (mtt) REVERT: C 977 VAL cc_start: 0.8629 (t) cc_final: 0.8416 (t) REVERT: D 512 MET cc_start: 0.7597 (mtp) cc_final: 0.7089 (ttm) REVERT: D 857 MET cc_start: 0.7538 (ttm) cc_final: 0.6897 (mtt) REVERT: D 892 MET cc_start: 0.7876 (tpt) cc_final: 0.7526 (tpt) REVERT: D 977 VAL cc_start: 0.8718 (t) cc_final: 0.8479 (t) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.1826 time to fit residues: 124.7473 Evaluate side-chains 309 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 30 optimal weight: 30.0000 chunk 287 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 286 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 214 optimal weight: 50.0000 chunk 139 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 345 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 850 GLN C 168 HIS ** D 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.158408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.142394 restraints weight = 158300.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140968 restraints weight = 137366.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.138525 restraints weight = 119603.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.138599 restraints weight = 108078.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.138555 restraints weight = 80581.073| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4102 r_free = 0.4102 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32316 Z= 0.131 Angle : 0.637 10.051 43760 Z= 0.333 Chirality : 0.047 0.304 4892 Planarity : 0.005 0.067 5612 Dihedral : 5.676 31.200 4428 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.90 % Favored : 93.00 % Rotamer: Outliers : 0.24 % Allowed : 1.48 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.12), residues: 4068 helix: -1.63 (0.11), residues: 1672 sheet: -0.97 (0.22), residues: 520 loop : -2.44 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 881 TYR 0.018 0.002 TYR A 825 PHE 0.017 0.001 PHE B1069 TRP 0.018 0.001 TRP A 827 HIS 0.010 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00304 (32316) covalent geometry : angle 0.63714 (43760) hydrogen bonds : bond 0.03433 ( 1004) hydrogen bonds : angle 5.22776 ( 2949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.6795 (mmp) cc_final: 0.6167 (mmp) REVERT: A 512 MET cc_start: 0.7472 (mtp) cc_final: 0.6847 (ttm) REVERT: A 621 ILE cc_start: 0.7864 (mt) cc_final: 0.7661 (mt) REVERT: A 857 MET cc_start: 0.7487 (ttm) cc_final: 0.6974 (mtp) REVERT: A 977 VAL cc_start: 0.8652 (t) cc_final: 0.8378 (t) REVERT: B 385 GLN cc_start: 0.8639 (pm20) cc_final: 0.8260 (mp10) REVERT: B 512 MET cc_start: 0.7467 (mtp) cc_final: 0.6775 (ttm) REVERT: B 857 MET cc_start: 0.7620 (ttm) cc_final: 0.6944 (mtt) REVERT: B 977 VAL cc_start: 0.8598 (t) cc_final: 0.8362 (t) REVERT: C 385 GLN cc_start: 0.8676 (pm20) cc_final: 0.8435 (mp10) REVERT: C 512 MET cc_start: 0.7498 (mtp) cc_final: 0.6849 (ttm) REVERT: C 857 MET cc_start: 0.7636 (ttm) cc_final: 0.6889 (mtt) REVERT: C 892 MET cc_start: 0.8267 (tpt) cc_final: 0.8017 (tpp) REVERT: C 977 VAL cc_start: 0.8686 (t) cc_final: 0.8454 (t) REVERT: D 512 MET cc_start: 0.7483 (mtp) cc_final: 0.6837 (ttm) REVERT: D 857 MET cc_start: 0.7572 (ttm) cc_final: 0.6821 (mtt) REVERT: D 977 VAL cc_start: 0.8674 (t) cc_final: 0.8415 (t) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1712 time to fit residues: 121.4792 Evaluate side-chains 314 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 94 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 245 optimal weight: 0.0670 chunk 327 optimal weight: 30.0000 chunk 391 optimal weight: 4.9990 chunk 289 optimal weight: 0.4980 overall best weight: 2.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS B 9 GLN B 136 HIS C 136 HIS D 9 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.158835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.142354 restraints weight = 136178.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.141393 restraints weight = 120676.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.138236 restraints weight = 116447.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.138111 restraints weight = 117114.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.137376 restraints weight = 95140.592| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32316 Z= 0.123 Angle : 0.620 8.714 43760 Z= 0.323 Chirality : 0.047 0.316 4892 Planarity : 0.005 0.067 5612 Dihedral : 5.407 30.204 4428 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.05 % Rotamer: Outliers : 0.24 % Allowed : 1.63 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.12), residues: 4068 helix: -1.32 (0.12), residues: 1676 sheet: -0.82 (0.22), residues: 512 loop : -2.26 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 729 TYR 0.023 0.002 TYR A 801 PHE 0.022 0.001 PHE C 959 TRP 0.017 0.001 TRP A 827 HIS 0.012 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00283 (32316) covalent geometry : angle 0.61983 (43760) hydrogen bonds : bond 0.03135 ( 1004) hydrogen bonds : angle 4.92610 ( 2949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.7369 (mtp) cc_final: 0.6749 (ttm) REVERT: A 621 ILE cc_start: 0.7719 (mt) cc_final: 0.7496 (mt) REVERT: A 857 MET cc_start: 0.7598 (ttm) cc_final: 0.7193 (mtp) REVERT: A 977 VAL cc_start: 0.8580 (t) cc_final: 0.8321 (t) REVERT: B 422 ARG cc_start: 0.7369 (mtp180) cc_final: 0.7044 (mtt180) REVERT: B 512 MET cc_start: 0.7325 (mtp) cc_final: 0.6665 (ttm) REVERT: B 621 ILE cc_start: 0.7743 (mt) cc_final: 0.7511 (mt) REVERT: B 666 MET cc_start: 0.6632 (mpp) cc_final: 0.5874 (ptt) REVERT: B 857 MET cc_start: 0.7697 (ttm) cc_final: 0.7225 (mtp) REVERT: B 977 VAL cc_start: 0.8535 (t) cc_final: 0.8312 (t) REVERT: C 512 MET cc_start: 0.7484 (mtp) cc_final: 0.6776 (ttm) REVERT: C 621 ILE cc_start: 0.7716 (mt) cc_final: 0.7512 (mt) REVERT: C 857 MET cc_start: 0.7697 (ttm) cc_final: 0.7024 (mtt) REVERT: C 977 VAL cc_start: 0.8618 (t) cc_final: 0.8377 (t) REVERT: D 422 ARG cc_start: 0.7389 (mtp180) cc_final: 0.7089 (mtt180) REVERT: D 512 MET cc_start: 0.7372 (mtp) cc_final: 0.6734 (ttm) REVERT: D 666 MET cc_start: 0.6742 (mpp) cc_final: 0.5933 (ptt) REVERT: D 857 MET cc_start: 0.7425 (ttm) cc_final: 0.6766 (mtt) REVERT: D 892 MET cc_start: 0.8279 (tpp) cc_final: 0.7959 (tpt) REVERT: D 977 VAL cc_start: 0.8594 (t) cc_final: 0.8322 (t) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1775 time to fit residues: 119.0291 Evaluate side-chains 321 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 116 optimal weight: 20.0000 chunk 157 optimal weight: 50.0000 chunk 299 optimal weight: 0.9980 chunk 291 optimal weight: 0.0070 chunk 44 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 286 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 HIS C 168 HIS ** D 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.159383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144588 restraints weight = 202693.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.144004 restraints weight = 158808.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.143593 restraints weight = 92697.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.143494 restraints weight = 88683.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.143554 restraints weight = 65212.395| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32316 Z= 0.121 Angle : 0.622 7.971 43760 Z= 0.320 Chirality : 0.047 0.324 4892 Planarity : 0.004 0.049 5612 Dihedral : 5.252 31.238 4428 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.28 % Rotamer: Outliers : 0.24 % Allowed : 0.98 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.12), residues: 4068 helix: -1.06 (0.12), residues: 1656 sheet: -0.79 (0.22), residues: 520 loop : -2.14 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 729 TYR 0.032 0.002 TYR B 704 PHE 0.019 0.001 PHE D 959 TRP 0.013 0.001 TRP A 84 HIS 0.007 0.001 HIS D 537 Details of bonding type rmsd covalent geometry : bond 0.00281 (32316) covalent geometry : angle 0.62169 (43760) hydrogen bonds : bond 0.03037 ( 1004) hydrogen bonds : angle 4.82380 ( 2949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.7337 (mtp) cc_final: 0.6787 (ttm) REVERT: A 857 MET cc_start: 0.7680 (ttm) cc_final: 0.7225 (mtp) REVERT: A 892 MET cc_start: 0.7987 (tpt) cc_final: 0.7549 (tpt) REVERT: A 925 THR cc_start: 0.8949 (m) cc_final: 0.8704 (m) REVERT: A 977 VAL cc_start: 0.8527 (t) cc_final: 0.8289 (t) REVERT: B 512 MET cc_start: 0.7327 (mtp) cc_final: 0.6756 (ttm) REVERT: B 666 MET cc_start: 0.6384 (mpp) cc_final: 0.5894 (ptt) REVERT: B 857 MET cc_start: 0.7660 (ttm) cc_final: 0.7116 (mtp) REVERT: B 892 MET cc_start: 0.7854 (tpt) cc_final: 0.7429 (tpt) REVERT: B 977 VAL cc_start: 0.8533 (t) cc_final: 0.8322 (t) REVERT: C 417 MET cc_start: 0.7910 (mmp) cc_final: 0.7682 (mmm) REVERT: C 512 MET cc_start: 0.7459 (mtp) cc_final: 0.6842 (ttm) REVERT: C 857 MET cc_start: 0.7748 (ttm) cc_final: 0.6983 (mtt) REVERT: C 977 VAL cc_start: 0.8599 (t) cc_final: 0.8375 (t) REVERT: D 512 MET cc_start: 0.7367 (mtp) cc_final: 0.6834 (ttm) REVERT: D 666 MET cc_start: 0.6322 (mpp) cc_final: 0.5924 (ptt) REVERT: D 857 MET cc_start: 0.7697 (ttm) cc_final: 0.6968 (mtt) REVERT: D 892 MET cc_start: 0.7937 (tpp) cc_final: 0.7403 (tpt) REVERT: D 977 VAL cc_start: 0.8602 (t) cc_final: 0.8348 (t) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1750 time to fit residues: 113.5289 Evaluate side-chains 318 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 262 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 157 optimal weight: 0.4980 chunk 194 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 398 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 393 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN C 410 HIS C 645 ASN D 410 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.157188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.142324 restraints weight = 193700.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.141304 restraints weight = 160134.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140697 restraints weight = 102321.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.140765 restraints weight = 95703.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.140474 restraints weight = 79039.091| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4124 r_free = 0.4124 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32316 Z= 0.162 Angle : 0.653 8.703 43760 Z= 0.338 Chirality : 0.048 0.339 4892 Planarity : 0.004 0.050 5612 Dihedral : 5.349 30.813 4428 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 0.24 % Allowed : 1.10 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.12), residues: 4068 helix: -1.02 (0.12), residues: 1680 sheet: -0.80 (0.22), residues: 520 loop : -2.14 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 729 TYR 0.016 0.002 TYR C 124 PHE 0.015 0.002 PHE D 959 TRP 0.014 0.001 TRP C 84 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00374 (32316) covalent geometry : angle 0.65324 (43760) hydrogen bonds : bond 0.03161 ( 1004) hydrogen bonds : angle 4.93186 ( 2949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.6844 (tmm) cc_final: 0.6638 (ptm) REVERT: A 512 MET cc_start: 0.7385 (mtp) cc_final: 0.6807 (ttm) REVERT: A 621 ILE cc_start: 0.7497 (mp) cc_final: 0.7044 (mt) REVERT: A 857 MET cc_start: 0.7729 (ttm) cc_final: 0.7233 (mtp) REVERT: A 892 MET cc_start: 0.8153 (tpt) cc_final: 0.7894 (tpp) REVERT: A 925 THR cc_start: 0.8995 (m) cc_final: 0.8727 (m) REVERT: A 977 VAL cc_start: 0.8625 (t) cc_final: 0.8399 (t) REVERT: B 327 MET cc_start: 0.6829 (tmm) cc_final: 0.6615 (ptm) REVERT: B 417 MET cc_start: 0.6583 (mmp) cc_final: 0.5996 (mmp) REVERT: B 512 MET cc_start: 0.7388 (mtp) cc_final: 0.6784 (ttm) REVERT: B 621 ILE cc_start: 0.7504 (mp) cc_final: 0.7112 (mt) REVERT: B 666 MET cc_start: 0.6674 (mpp) cc_final: 0.6342 (ptt) REVERT: B 857 MET cc_start: 0.7674 (ttm) cc_final: 0.7124 (mtp) REVERT: B 892 MET cc_start: 0.8187 (tpt) cc_final: 0.7813 (tpp) REVERT: B 977 VAL cc_start: 0.8608 (t) cc_final: 0.8393 (t) REVERT: C 417 MET cc_start: 0.7871 (mmp) cc_final: 0.7550 (mmm) REVERT: C 512 MET cc_start: 0.7483 (mtp) cc_final: 0.6854 (ttm) REVERT: C 621 ILE cc_start: 0.7578 (mp) cc_final: 0.7159 (mt) REVERT: C 857 MET cc_start: 0.7752 (ttm) cc_final: 0.6992 (mtt) REVERT: C 892 MET cc_start: 0.8490 (tpp) cc_final: 0.8285 (tpt) REVERT: C 977 VAL cc_start: 0.8683 (t) cc_final: 0.8468 (t) REVERT: D 327 MET cc_start: 0.6809 (tmm) cc_final: 0.6604 (ptm) REVERT: D 512 MET cc_start: 0.7402 (mtp) cc_final: 0.6807 (ttm) REVERT: D 666 MET cc_start: 0.6706 (mpp) cc_final: 0.6392 (ptt) REVERT: D 857 MET cc_start: 0.7727 (ttm) cc_final: 0.6936 (mtt) REVERT: D 892 MET cc_start: 0.7961 (tpp) cc_final: 0.7609 (tpt) REVERT: D 977 VAL cc_start: 0.8664 (t) cc_final: 0.8429 (t) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1707 time to fit residues: 106.1153 Evaluate side-chains 291 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 70 optimal weight: 40.0000 chunk 273 optimal weight: 8.9990 chunk 356 optimal weight: 0.3980 chunk 218 optimal weight: 6.9990 chunk 401 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 362 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 382 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 HIS C 645 ASN D 47 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.157131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.141926 restraints weight = 185294.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.139910 restraints weight = 162967.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.139027 restraints weight = 122929.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.139019 restraints weight = 120548.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.138967 restraints weight = 87358.730| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4113 r_free = 0.4113 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4113 r_free = 0.4113 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32316 Z= 0.162 Angle : 0.664 9.008 43760 Z= 0.342 Chirality : 0.048 0.353 4892 Planarity : 0.005 0.059 5612 Dihedral : 5.377 31.350 4428 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 0.24 % Allowed : 0.71 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.12), residues: 4068 helix: -1.00 (0.12), residues: 1684 sheet: -0.80 (0.22), residues: 520 loop : -2.09 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 729 TYR 0.032 0.002 TYR C 579 PHE 0.015 0.002 PHE D 959 TRP 0.014 0.001 TRP A 84 HIS 0.005 0.001 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00374 (32316) covalent geometry : angle 0.66389 (43760) hydrogen bonds : bond 0.03212 ( 1004) hydrogen bonds : angle 4.93185 ( 2949) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.6554 (mmp) cc_final: 0.6024 (mmp) REVERT: A 512 MET cc_start: 0.7380 (mtp) cc_final: 0.6806 (ttm) REVERT: A 621 ILE cc_start: 0.7765 (mp) cc_final: 0.7401 (mt) REVERT: A 857 MET cc_start: 0.7727 (ttm) cc_final: 0.7279 (mtp) REVERT: A 892 MET cc_start: 0.8082 (tpt) cc_final: 0.7807 (tpp) REVERT: A 925 THR cc_start: 0.9124 (m) cc_final: 0.8902 (m) REVERT: A 977 VAL cc_start: 0.8641 (t) cc_final: 0.8419 (t) REVERT: B 327 MET cc_start: 0.7112 (tmm) cc_final: 0.6718 (ptm) REVERT: B 512 MET cc_start: 0.7355 (mtp) cc_final: 0.6777 (ttm) REVERT: B 621 ILE cc_start: 0.7745 (mp) cc_final: 0.7401 (mt) REVERT: B 857 MET cc_start: 0.7661 (ttm) cc_final: 0.7092 (mtp) REVERT: B 892 MET cc_start: 0.8142 (tpt) cc_final: 0.7721 (tpp) REVERT: B 977 VAL cc_start: 0.8562 (t) cc_final: 0.8326 (t) REVERT: C 512 MET cc_start: 0.7434 (mtp) cc_final: 0.6847 (ttm) REVERT: C 621 ILE cc_start: 0.7749 (mp) cc_final: 0.7421 (mt) REVERT: C 857 MET cc_start: 0.7746 (ttm) cc_final: 0.6959 (mtt) REVERT: C 977 VAL cc_start: 0.8609 (t) cc_final: 0.8379 (t) REVERT: D 327 MET cc_start: 0.7092 (tmm) cc_final: 0.6645 (ptm) REVERT: D 512 MET cc_start: 0.7431 (mtp) cc_final: 0.6916 (ttm) REVERT: D 621 ILE cc_start: 0.7546 (mp) cc_final: 0.7126 (mt) REVERT: D 857 MET cc_start: 0.7567 (ttm) cc_final: 0.6818 (mtt) REVERT: D 977 VAL cc_start: 0.8680 (t) cc_final: 0.8443 (t) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1645 time to fit residues: 101.4286 Evaluate side-chains 294 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 359 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 95 optimal weight: 0.9990 chunk 384 optimal weight: 1.9990 chunk 41 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 275 optimal weight: 10.0000 chunk 396 optimal weight: 0.0040 chunk 115 optimal weight: 20.0000 chunk 340 optimal weight: 10.0000 chunk 256 optimal weight: 20.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.158180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.141396 restraints weight = 149917.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.139864 restraints weight = 139504.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.137746 restraints weight = 139645.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.137745 restraints weight = 118007.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.137157 restraints weight = 101063.675| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32316 Z= 0.131 Angle : 0.639 9.221 43760 Z= 0.329 Chirality : 0.047 0.348 4892 Planarity : 0.004 0.052 5612 Dihedral : 5.216 30.754 4428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.92 % Favored : 92.98 % Rotamer: Outliers : 0.24 % Allowed : 0.39 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.13), residues: 4068 helix: -0.95 (0.12), residues: 1680 sheet: -0.69 (0.23), residues: 516 loop : -1.99 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 362 TYR 0.032 0.002 TYR D 704 PHE 0.023 0.001 PHE A 405 TRP 0.014 0.001 TRP D 84 HIS 0.006 0.001 HIS D 537 Details of bonding type rmsd covalent geometry : bond 0.00303 (32316) covalent geometry : angle 0.63924 (43760) hydrogen bonds : bond 0.03046 ( 1004) hydrogen bonds : angle 4.77418 ( 2949) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.5234 (tptp) cc_final: 0.4394 (mmmt) REVERT: A 327 MET cc_start: 0.7147 (tmm) cc_final: 0.6651 (ptm) REVERT: A 417 MET cc_start: 0.6751 (mmp) cc_final: 0.6042 (tpp) REVERT: A 512 MET cc_start: 0.7494 (mtp) cc_final: 0.7049 (ttm) REVERT: A 621 ILE cc_start: 0.7708 (mp) cc_final: 0.7348 (mt) REVERT: A 857 MET cc_start: 0.7793 (ttm) cc_final: 0.7366 (mtp) REVERT: A 925 THR cc_start: 0.9090 (m) cc_final: 0.8883 (m) REVERT: A 977 VAL cc_start: 0.8683 (t) cc_final: 0.8435 (t) REVERT: B 327 MET cc_start: 0.7159 (tmm) cc_final: 0.6610 (ptm) REVERT: B 512 MET cc_start: 0.7494 (mtp) cc_final: 0.7025 (ttm) REVERT: B 621 ILE cc_start: 0.7766 (mp) cc_final: 0.7395 (mt) REVERT: B 742 CYS cc_start: 0.6637 (m) cc_final: 0.6284 (t) REVERT: B 857 MET cc_start: 0.7806 (ttm) cc_final: 0.7199 (mtp) REVERT: B 892 MET cc_start: 0.8290 (tpt) cc_final: 0.7814 (tpt) REVERT: B 977 VAL cc_start: 0.8558 (t) cc_final: 0.8326 (t) REVERT: C 512 MET cc_start: 0.7566 (mtp) cc_final: 0.7054 (ttm) REVERT: C 621 ILE cc_start: 0.7705 (mp) cc_final: 0.7388 (mt) REVERT: C 857 MET cc_start: 0.7771 (ttm) cc_final: 0.7079 (mtt) REVERT: C 892 MET cc_start: 0.8145 (tpt) cc_final: 0.7848 (tpp) REVERT: C 977 VAL cc_start: 0.8630 (t) cc_final: 0.8394 (t) REVERT: D 327 MET cc_start: 0.7173 (tmm) cc_final: 0.6704 (ptm) REVERT: D 405 PHE cc_start: 0.6813 (m-10) cc_final: 0.6603 (m-10) REVERT: D 512 MET cc_start: 0.7517 (mtp) cc_final: 0.7062 (ttm) REVERT: D 621 ILE cc_start: 0.7569 (mp) cc_final: 0.7192 (mt) REVERT: D 857 MET cc_start: 0.7755 (ttm) cc_final: 0.7300 (mtp) REVERT: D 873 LEU cc_start: 0.9077 (mm) cc_final: 0.8758 (mm) REVERT: D 977 VAL cc_start: 0.8708 (t) cc_final: 0.8457 (t) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1747 time to fit residues: 106.8682 Evaluate side-chains 286 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 211 optimal weight: 0.2980 chunk 248 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 chunk 33 optimal weight: 0.0270 chunk 321 optimal weight: 20.0000 chunk 88 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.161341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144960 restraints weight = 161388.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143794 restraints weight = 138720.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.141897 restraints weight = 98230.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140952 restraints weight = 105351.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.140170 restraints weight = 104330.837| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4125 r_free = 0.4125 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 32316 Z= 0.107 Angle : 0.617 7.500 43760 Z= 0.314 Chirality : 0.047 0.374 4892 Planarity : 0.004 0.053 5612 Dihedral : 4.937 30.629 4428 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 0.24 % Allowed : 0.18 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.13), residues: 4068 helix: -0.70 (0.13), residues: 1660 sheet: -0.56 (0.23), residues: 516 loop : -1.86 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 881 TYR 0.031 0.001 TYR B 704 PHE 0.033 0.001 PHE B 998 TRP 0.015 0.001 TRP C 84 HIS 0.013 0.001 HIS C 410 Details of bonding type rmsd covalent geometry : bond 0.00241 (32316) covalent geometry : angle 0.61724 (43760) hydrogen bonds : bond 0.02918 ( 1004) hydrogen bonds : angle 4.53411 ( 2949) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.5133 (tptp) cc_final: 0.4335 (mmmt) REVERT: A 327 MET cc_start: 0.7136 (tmm) cc_final: 0.6755 (ptt) REVERT: A 417 MET cc_start: 0.6627 (mmp) cc_final: 0.6018 (tpp) REVERT: A 512 MET cc_start: 0.7323 (mtp) cc_final: 0.6873 (ttm) REVERT: A 621 ILE cc_start: 0.7363 (mp) cc_final: 0.7000 (mt) REVERT: A 670 LEU cc_start: 0.8200 (mt) cc_final: 0.7993 (mp) REVERT: A 857 MET cc_start: 0.7632 (ttm) cc_final: 0.7053 (mtp) REVERT: A 892 MET cc_start: 0.8356 (tpt) cc_final: 0.7996 (tpp) REVERT: A 977 VAL cc_start: 0.8574 (t) cc_final: 0.8270 (t) REVERT: A 1070 ILE cc_start: 0.8973 (mm) cc_final: 0.8712 (mm) REVERT: B 327 MET cc_start: 0.7104 (tmm) cc_final: 0.6603 (ptm) REVERT: B 417 MET cc_start: 0.6790 (mmp) cc_final: 0.6064 (tpp) REVERT: B 512 MET cc_start: 0.7387 (mtp) cc_final: 0.6907 (ttm) REVERT: B 857 MET cc_start: 0.7628 (ttm) cc_final: 0.7089 (mtp) REVERT: B 892 MET cc_start: 0.8212 (tpt) cc_final: 0.7724 (tpt) REVERT: B 977 VAL cc_start: 0.8498 (t) cc_final: 0.8219 (t) REVERT: B 1070 ILE cc_start: 0.9176 (mm) cc_final: 0.8939 (mm) REVERT: C 512 MET cc_start: 0.7452 (mtp) cc_final: 0.6913 (ttm) REVERT: C 857 MET cc_start: 0.7666 (ttm) cc_final: 0.7197 (mtp) REVERT: C 977 VAL cc_start: 0.8587 (t) cc_final: 0.8359 (t) REVERT: D 411 MET cc_start: 0.7388 (tpp) cc_final: 0.7159 (tpp) REVERT: D 512 MET cc_start: 0.7374 (mtp) cc_final: 0.6902 (ttm) REVERT: D 790 PHE cc_start: 0.7200 (t80) cc_final: 0.6984 (t80) REVERT: D 823 MET cc_start: 0.7887 (pmm) cc_final: 0.7482 (pmm) REVERT: D 857 MET cc_start: 0.7694 (ttm) cc_final: 0.7331 (mtp) REVERT: D 882 LEU cc_start: 0.8504 (mt) cc_final: 0.7808 (mt) REVERT: D 892 MET cc_start: 0.8262 (tpt) cc_final: 0.7953 (tpp) REVERT: D 977 VAL cc_start: 0.8616 (t) cc_final: 0.8310 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1685 time to fit residues: 110.6645 Evaluate side-chains 309 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 160 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 400 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 303 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 350 optimal weight: 0.6980 chunk 271 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.161565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.145697 restraints weight = 159113.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.144227 restraints weight = 135247.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.141342 restraints weight = 115224.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140907 restraints weight = 127139.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.139859 restraints weight = 108492.675| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4119 r_free = 0.4119 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.4119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32316 Z= 0.105 Angle : 0.607 8.911 43760 Z= 0.307 Chirality : 0.047 0.368 4892 Planarity : 0.004 0.053 5612 Dihedral : 4.801 30.591 4428 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 0.27 % Allowed : 0.12 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4068 helix: -0.56 (0.13), residues: 1664 sheet: -0.26 (0.23), residues: 540 loop : -1.78 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 881 TYR 0.021 0.001 TYR A 801 PHE 0.031 0.001 PHE B 998 TRP 0.012 0.001 TRP D 84 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd covalent geometry : bond 0.00240 (32316) covalent geometry : angle 0.60736 (43760) hydrogen bonds : bond 0.02840 ( 1004) hydrogen bonds : angle 4.46044 ( 2949) =============================================================================== Job complete usr+sys time: 4635.16 seconds wall clock time: 81 minutes 33.36 seconds (4893.36 seconds total)